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Crystal structure of a complex between G protein beta gamma dimer and an inhibitory Nanobody regulator
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1A0R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 277.15 25-30% (w/v) PEG 3350 in 0.1-0.2 M Bis-Tris-HCl, pH 5.5-5.7, and 0.2-0.3 M MgCl2
Crystal Properties Matthews coefficient Solvent content 2.38 48.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.66 α = 90 b = 77.23 β = 109.8 c = 101.66 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100.15 PIXEL DECTRIS EIGER X 16M 2017-07-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97918 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.34 47.82 99.6 0.22 0.991 6.28 4.31 42434
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.34 2.4 99.8 1.77 0.507 1.05 4.43
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1A0R 2.34 47.82 42434 2234 99.65 0.20283 0.20034 0.2084 0.24906 0.2527 RANDOM 52.181
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.11 -1.95 3.38 -1.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.312 r_dihedral_angle_4_deg 17.718 r_dihedral_angle_3_deg 14.897 r_long_range_B_refined 9.97 r_long_range_B_other 9.966 r_dihedral_angle_1_deg 7.107 r_scangle_other 6.105 r_mcangle_it 5.635 r_mcangle_other 5.634 r_scbond_it 3.869
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.312 r_dihedral_angle_4_deg 17.718 r_dihedral_angle_3_deg 14.897 r_long_range_B_refined 9.97 r_long_range_B_other 9.966 r_dihedral_angle_1_deg 7.107 r_scangle_other 6.105 r_mcangle_it 5.635 r_mcangle_other 5.634 r_scbond_it 3.869 r_scbond_other 3.869 r_mcbond_it 3.637 r_mcbond_other 3.635 r_angle_refined_deg 1.574 r_angle_other_deg 0.988 r_chiral_restr 0.092 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7872 Nucleic Acid Atoms Solvent Atoms 396 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing